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QIAGEN CLC Genomics Server 10.0.2

Release date: 2018-12-06

Shared with workbenches

Bug fixes

  • Workbench response times after logging into a QIAGEN CLC Genomics Server have been improved in the situation where many server jobs, submitted from the Workbench, had completed since the last login.
  • Fixed a bug where the "Unaligned end" field provided in the Breakpoint track output of the Indel and Structural Variants tool was left blank when the value should have been "Mixed consensus" on all but one chromosome. The field is now filled for all chromosomes.
  • Fixed a issue with the Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools that caused a small minority of variants to go unreported under certain conditions expected to arise rarely.
  • Fixed a bug in the Identify Candidate Variants tool where no results were returned when one or more criteria used a comparison operator with more than one term (e.g. ">=", "abs value <").
  • Specifying a reference cache size greater than 2GB was not possible when using a readmapper.properties file.
  • Fixed a concurrency bug in the Copy Number Variant Detection tool, which very rarely resulted in the tool reporting all low-coverage targets on one or more chromosomes as false positive deletions. (Biomedical enabled Genomics Server only)
  • Various minor bugfixes.

Compatibility

The following are the corresponding clients for the QIAGEN CLC Genomics Server 10.0.2.

  • QIAGEN CLC Genomics Workbench 11.0.2
  • Biomedical Genomics Workbench 5.0.2
  • CLC Command Line Tools 5.0.2

We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 11.0 and 11.0.1, Biomedical Genomics Workbench 5.0 and 5.0.1, and CLC Command Line Tools 5.0 and 5.0.1 can also connect to QIAGEN CLC Genomics Server 10.0.2. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

Advanced notice

  • SOLiD colorspace data support, including import, is not available in the the next major release line of the software.
  • Roche 454 NGS import is now a legacy tool. We have retained it in the next major release line of the software, but it may be retired in a future release.

If you are concerned about these changes, please contact the QIAGEN Bioinformatics team (ts-bioinformatics@qiagen.com).

 

CLC Server Command Line Tools

This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 10.0.2.

Compatibility

CLC Command Line Tools 5.0.2 is the corresponding client for QIAGEN CLC Genomics Server 10.0.2.

CLC Command Line Tools 5.0.2 can also act as a client for the QIAGEN CLC Genomics Server 10.0 and 10.0.1. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.



QIAGEN CLC Genomics Server 10.0.1

Release date: 2018-03-14

Server specific

  • The option for exporting a history csv file when configuring the User-selected Input data (CLC data location) value is now listed as "History CSV (.csv)". It was shown as "Table Comma Separate Values (.csv) in CQIAGEN LC Genomics Server 10.0.
  • Fixed a bug preventing the Genomics server from (re-) starting on a Spanish Windows installation

Shared with workbenches

  • Implemented the 3' HGVS compliance rule for c. annotation of variants:

- When doing c. annotations (DNA-level HGVS) we annotate insertions that really are duplications as such.
- For c. annotations we furthermore fulfill the 3' rule for insertions, deletions and duplications.
- When determining amino acid changes, the 3' rule is applied to the DNA change first. This may shift a variant in or out of the coding region, and that will affect whether or not we consider it as an amino acid change.

The 3' rule for p. annotations were previously fulfilled and are not affected by this fix.

  • Fixed an issue where workflows with a VCF export element could not be run from a workbench on the QIAGEN CLC Genomics Server.
  • Fixed a bug in the VCF (Variant Calling Format) file format exporter that affected the QUAL score of the variant. Previously, the variant QUAL score was set to be the maximum QUAL score of all alleles (regardless of whether it was a reference allele or not). In some instances, e.g., when there are two alleles and one has poor QUAL score, this choice was suboptimal. Instead, the variant QUAL score is now chosen as the maximum QUAL scores among all non-reference variants.
  • Fixed an issue where the RNA-Seq Analysis tool would show an error if the first chromosome or contig contained no transcripts and the "Calculate expression for genes without transcripts" option was used.
  • Fixed an issue where the RNA-Seq Analysis tool would sometimes generate TE tracks that could not be used in downstream tools. The error occurred when the "Calculate expression for genes without transcripts" option was used on a gene track where two genes had the same name, one of the genes contained the other, and neither gene had a transcript.
  • Fixed an issue with the Trim Reads tool used in a workflow with multiple Trim adapter lists as input: all but the first list input were previously silently ignored, but the workflow now gives users a warning message.
  • Fixed an issue where importing a Trim Adapter List with an adapter with "Discard the read (end matches at 3')" was imported incorrectly.
  • Fixed an issue that could cause some third party plugins to fail trying to retrieve the fastq exporter.
  • Fixed an issue where domain annotations added by the Pfam Domain Search tool started one amino acid later than expected. The corresponding start position in the table produced by the tool was correct.
Compatibility

The following are the corresponding clients for the QIAGEN CLC Genomics Server 10.0.1

  • QIAGEN CLC Genomics Workbench 11.0.1
  • Biomedical Genomics Workbench 5.0.1
  • CLC Command Line Tools 5.0.1

We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 11.0, Biomedical Genomics Workbench 5.0, and CLC Command Line Tools 5.0 can also connect to QIAGEN CLC Genomics Server 10.0.1. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

Advanced notice

  • SOLiD colorspace data support, including import, will be retired and will not be available in the the next major release of the software.
  • Roche 454 NGS import is now a legacy tool. We plan to retain it in the next major release of the software, but it may be retired in a future release.

If you are concerned about these changes, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).

 

CLC Server Command Line Tools

This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 10.0.1.

Compatibility

CLC Command Line Tools 5.0.1 is the corresponding client for QIAGEN CLC Genomics Server 10.0.1

CLC Command Line Tools 5.0.1 can also act as a client for the QIAGEN CLC Genomics Server 10.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.

Advanced notice

  • With a release planned for late 2018, only 64 bit versions of the CLC Server Command Line Tools will be made available. The 32 bit version will be discontinued from that time.
  • The NGS import tool ngs_import_solid is now a legacy tool. It will not be available from the the next major release of this software.
  • The NGS import tool ngs_import_roche454 is now a legacy tool. We plan to retain it in the next major release of the software, but it may be retired in a future release.

If you are concerned about these changes, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).



QIAGEN CLC Genomics Server 10.0.0

Release date: 2017-11-21

Server specific

Improvements and new features

  • "Output file from CL" in External Applications (EA) configurations now supports the configuration of parameters for exporters. Existing EA configurations will continue to work using the older configuration, exactly as on older versions of the QIAGEN CLC Genomics Server. Only if a change is made, and saved, to an existing configuration of an "Output file from CL" entry, will the exporter be updated to support the configuration of parameters.
  • The report generated by the "check setup" functionality now lists information about the installed licenses.
  • External Applications can now be organized into subfolders of the External Applications area of the Workbench Toolbox.
  • The time needed to complete the "Saving results" step of a workflow running on a QIAGEN CLC Genomics Server has been shortened.
  • The column headings in the table containing statistics for each mapping, optionally produced by the QC for Read Mapping Tool (Bx-enabled servers only) and the Create Detailed Mapping Report tool, have been made more descriptive.
  • Fixed an issue where the removal of terminated sub batch-processes from the Workbench Processes tab before the master process finished would produce an error dialog.
  • Improved performance for several tools when handling genomes with many chromosomes. Examples include Annotate with Overlap Information, the BED Exporter, Filter Annotations On Name, and Motif Search and for Bx-enabled Servers, Add Fold Changes and Add Information from Overlapping Variants.

Bug fixes

  • An issue was fixed that caused a Workbench restart to be necessary for running an External Application if it had been changed on the QIAGEN CLC Genomics Server since the time the Workbench user had logged into that server.
  • Fixed an issue where only one post-processing step in an External Application configuration was listed next to an "Output file from CL" parameter, even when multiple post-processing steps had been linked to it.
  • Fixed an issue where export to CLC or zip format led to an error when permissions were set on both the source QIAGEN CLC Genomics Server file location and also on the Import/Export location the data was to be exported to.
  • Fixed an issue affecting unknown users trying to log into the QIAGEN CLC Genomics Server where the server was incorrectly configured with LDAP with Bind DN while pointing towards an Active Directory (AD) backend. Such logins will now fail. Previously an anonymous login would result.

Shared with workbenches

Improvements and new features

 
  • Trim Reads:
    • The Trim Sequences tool has been renamed to Trim Reads.
    • A new option has been added to the Trim Reads tool: "Automatic read-through adapter trimming". This option makes it possible to automatically identify overlap in paired reads and will trim the region that is not part of that overlap. This option is turned on by default. This new default affects workflows that include Trim Reads (or by its former name: Trim Sequences); the parameter will be turned on and locked by default. For a Biomedical-enabled server, this change also affects the inbuilt workflow Prepare Raw Data.
  • Trimming adaptor:
    • The New Trim Adapter List dialog has been updated to a new and more user-friendly interface.
    • It is now possible to reverse complement an adapter sequence with a "Reverse Complement" button to the right of the sequence field.
    • It is now possible to specify whether the trim should be performed on all reads, or only on the first or second read of a pair.
    • A visual shows the adapter and the sequence being trimmed in relation to the rest of the sequence depending on the option chosen when an adapter is found.
  • RNA-Seq Analysis:
    • RPKM is now always calculated when running the RNA-Seq Analysis tool with the options "Genome annotated with genes only" and "One reference sequence per transcript".
    • The default for the reference type parameter is now "Genome annotated with genes and transcripts".
    • In the RNA-Seq Analysis tool, the option "Calculate RPKM for genes without transcripts" has been renamed to "Calculate expression for genes without transcripts".
    • The behavior of the RNA-Seq Analysis tool has been changed when the option “Genome annotated with genes and transcripts” is used together with the option “Calculate expression for genes without transcripts".
      • The counts of genes without transcripts are calculated. Previously only the TPM and RPKM were calculated.
      • For a gene without a corresponding transcript, where that gene is overlapped by the intron of another gene, reads aligning to this region are counted towards the expression of the gene without the transcript. Previously such reads were counted as belonging to the intronic region of the overlapping gene.
      • A single-exon transcript for each gene without transcripts is now added to the output TE track.
  • Paired sequence lists can now be exported to 2 fastq formatted files, one file containing the first member of each pair, the other containing the second member. This is now the default for Fastq Export when exporting paired data.
  • The history of a data element can now be exported as a CSV format file.
  • An option to include reads that partially overlap variants has been added to the Identify Known Mutations from Sample Mappings tool, enabling detection of variants that are longer than the reads.
  • The Identify Known Mutations from Sample Mappings tool has been made slightly more strict when handling insertions and replacements, requiring reads to overlap adjacent reference positions to be counted as fully covering the variant.
  • The speed of the Illumina High-Throughput Sequencing Import has been substantially improved. The largest gains are seen on paired read files compressed by gzip with speed improvements of up to 30%.
  • The Download Pfam Database tool now downloads version 31. Updates can now be made independently of the release of the QIAGEN CLC Genomics Server, so the version available for download could change over time from the one recorded here.
  • Clicking "Select genes in other views" in a Volcano Plot with an empty selection no longer gives an error message.
  • When exporting files to SAM or BAM format files, information is now entered into the optional fields NM (edit distance) and MD (mismatch string).
  • Importing a GO annotation file with the Standard Import tool, specifying the format "Generic annotation file for expression data", now fails with an informative warning if any of the GO annotations are truncated.
  • Warnings are now reported if truncated GO annotations are found when opening data created by the Create Expression Browser tool.
  • NCBI blast executables are upgraded to version 2.6.0.
  • The Download Reference Genome Data tool now downloads genome annotations from GFF3 files instead of previously as GTF files. Genome annotations for Homo sapiens versions hg18 and hg19 are still downloaded as GTF files, as these are not available as GFF3 files.
  • HTML formatting tags are now removed during export of data to Excel .xlsx or .xls format. This change does not affect the export of hyperlinks.
  • This history information for data generated using the Identify Candidate Variants tool now  includes a match criteria field, recording if the option 'match all' or 'match any' was used.
  • Parameters for the Trim Sequences tool are now shown in the same order when running the tool from the Toolbox or within a workflow.
  • Map Reads to Reference now outputs an empty read mapping and report when the input contains 0 reads.
  • A warning message is now presented when the tool Extract Sequences is run with the "Extract to single sequences option" selected and more than 100 sequences would result.

Changes

  • The Roche 454 and SOLiD Import tools have been moved to the Legacy folder of the Workbench Toolbox.
  • The option "Search on both strands"  has been removed in the Trim Reads tool (formerly named Trim Sequences) and the Extract and Count tool.
  • The Create Mapping Graph tool has been modified so that the coverage of overlapping paired end reads is now only counted as one in the overlapping region, instead of two as done previously.
  • Removed the line "Total consensus length" from Detailed Mapping Report when using a Read Mapping Track as input, as these tracks do not contain consensus information.
  • The SAM and BAM Mapping Files importer now fails if there are reads with more than one primary alignment where both are marked as being the first in a pair or both are marked as being second in a pair.
  • The GCG sequence exporter has been removed. The GCG alignment exporter is unaffected by these changes.
  • The underlying read mapper and de novo binaries included in the QIAGEN CLC Genomics Server 10.0 are from QIAGEN CLC Assembly Cell 5.0.5.

Bug fixes

  • Fixed an issue where paired distances were calculated incorrectly for paired reads in Forward-Reverse orientation where there is adapter read-through. Paired distances can be seen in the report from the Map Reads to Reference tool and the RNA-Seq Analysis tool. The paired distance calculation is also used by the "auto-detect paired distances" option in these tools, although this issue is unlikely to affect the inferred distances.
  • Fixed a bug where the Amino Acid Changes tool would in some cases use the CDS reference instead of the RNA reference for annotating coding region changes. This would happen if the RNA and CDS annotations could not be matched, and it could cause variants in UTR regions to not be reported. The matching has now been improved by supporting the 'parent' field used by the GFF3 file format to pair CDS and RNA references.
  • Fixed a bug in the RNA-Seq Analysis tool where, when run in "Genes and transcripts" mode, and using "Total counts" as Expression value, the expression values reported for GE tracks would not include shared exon counts. Downstream analyses based on the Set Up Experiment tool could be affected by this issue. Using affected GE tracks as input to the following tools would *not* affect their results: Differential Expression for RNA-Seq, Create Heat Map for RNA-Seq and PCA for RNA-Seq.
  • Fixed an issue where the option to run the Differential Expression for RNA-Seq tool in batch mode was made available, leading to an error if it was selected.
  • Fixed an issue where the number of input samples to the Map Reads to References and Map Reads to Contigs tools would be silently limited to 120. The execution is now aborted with a warning message. Each analysis must be started with 120 samples maximum.
  • Fixed an issue with the mapping tool in the QIAGEN CLC Genomics Server, which is used in tools involving a mapping stage, such as  Map Reads to References,  Map Reads to Contigs and RNA-Seq Analysis, where length and similarity fraction cut-offs in some cases were ignored for reads longer than 500bp.
  • Fixed an issue with the InDels and Structural Variants that caused it to crash if it encountered a particular set of conditions relating to reads with deletions.
  • Fixed an issues with the InDels and Structural Variants tool duplicate breakpoints and variants were reported if reads mapping as broken pairs were included in the analysis.
  • An issue has been fixed so that it is now possible to export in BAM format reads that contain synonyms, for instance 'X' as synonym for 'N'.
  • Fixed bug which caused the fasta exporter to fail when exporting read mappings where one or more reference sequences have no reads mapped to it.
  • Fixed an issue that could cause exports of reports with line graphs to fail.
  • Fixed an issue where resetting the default parameter values when configuring the  Identify Candidate Variants tool did not work.
  • Fixed an issue that would prevent the Trim Sequences tool being run with certain length filter settings.
  • Fixed a bug where a cell containing multiple hyperlinked URLs caused export to Excel 2010 or Excel 97-2007 format to fail. Such cell contents are now written in plain text.
  • Contigs with Gap annotations covering regions longer than 10 bp can now be successfully exported to AGP format. Sequences containing such gaps will be split into separate contigs on export. This issue will be particularly of interest to those using the Join Contigs tool of the QIAGEN CLC Genome Finishing Module.
  • Fixed an issue where the Low Frequency Variant Detection tool could return NaN for the Probability value in rare instances for small datasets.
  • Fixed an issue with the QC for Target Sequencing tool (Bx-enabled servers only) and with the Create Statistics for Target Region tool, where "GC %" was reported as a ratio. It is now reported as a percentage.
  • Fixed an issue with the Add Information about Amino Acid Changes tool (Bx-enabled servers only) and the Amino Acid Changes tool, when used with a circular sequence with a CDS annotation placed across the origin. Variants outside such a wrapped annotation could previously be incorrectly annotated with coding region changes.
  • Fixed an issue with the Amino Acid Changes (Bx-enabled servers only) and the Amino Acid Changes tool, when used with a circular sequence with an intron across the origin. Previously, nearby variants were not annotated with coding region changes. Now, variants in such introns and that are within 2 nucleotides of the nearest exon will be annotated with coding region changes, if such changes are identified.
 

Plugin Notes for Biomedical-enabled server

  • A new plugin, QIAseq Targeted Panel Analysis 1.0, unifies the three QIAseq Targeted Panel plugins that were previously available: QIAseq DNA V3 Panel Analysis, QIAseq Targeted RNA Panel Analysis and QIAseq Targeted RNAscan Panel Analysis. The new plugin covers Targeted DNA for variant calling, Targeted RNA for differential expression and Targeted RNAscan for fusion gene detection with improvements resulting in more accurate variant calling and fusion gene detection.
 

Compatibility

The follow software are the corresponding clients for the QIAGEN CLC Genomics Server 10.0
      • QIAGEN CLC Genomics Workbench 11.0
      • Biomedical Genomics Workbench 5.0 (when the server has the Biomedical Extension)
      • CLC Command Line Tools 5.0

Advanced notice

  • SOLiD colorspace data support, including import, will be retired and will not be available in the the next major release of the software.
  • Roche 454 NGS import will be removed in a future release, but will still be available in the next major release of the software.
If you are concerned about the proposed changes, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).

CLC Server Command Line Tools

Changes to existing tools

export -e fastq
  • The default behavior of this tool has changed To maintain current behavior, scripts using this exporter must have "--export-paired-reads-to-two-files false  --one-file true" added to the command. 
  • --export-paired-reads-to-two-files" has been added. This parameter is set to true by default.
  • The default value of the --onefile parameter has been changed from true to false.  Note that the --onefile parameter cannot be set to true when the --export-paired-reads-to-two-files parameter is also set to true.  Having both set to true will cause the tool to fail with an error.
  • -e gcg                       has been removed.  Export to gcg format is no longer available
    mutation_tester_tool       
    •  --include-partially-covering-reads   has been added. When set to true, reads that partially cover variants will be included when calculating the results, enabling detection of variants longer than the reads. Set to false by default.
small_rna_sampling
    •  The default behavior of this tool has changed To maintain current behavior, scripts must have " --readthrough-trimming false" added to the command.
    • --readthrough-trimming   has been added. Detects overlaps in paired reads and trims the non-overlapping part away.
    •  --reverse-strand     has been removed.  This option is no longer used nor recognized. The default value in earlier versions was false.
trim
  •  The default behavior of this tool has changed To maintain current behavior, scripts must have " --readthrough-trimming false" added to the command.
  •  --readthrough-trimming  has been added and the default is set to true.   
  • --reverse-strand     has been removed. This option is no longer used nor recognized. The default value in earlier versions was false.
 

New features

export
  • -e history_csv           Export of history information to csv format has been added.
 

Advanced Notice

  • With a release planned for late 2018, only 64 bit versions of the QIAGEN CLC Server Command Line Tools will be made available. The 32 bit version will be discontinued from that time.
  • The NGS import tool ngs_import_solid is now a legacy tool and will be retired and will not be available in the the next major release of the software.
  • The NGS import tool ngs_import_roche454 is now a legacy tool and will be removed in a future release, but will be available in the next major release of the software.
 


QIAGEN CLC Genomics Server 9.1.3

Release date: 2018-12-06

Shared with workbenches

Bug fixes

  • Fixed a bug where the "Unaligned end" field provided in the Breakpoint track output of the Indel and Structural Variants tool was left blank when the value should have been "Mixed consensus" on all but one chromosome. The field is now filled for all chromosomes.
  • Fixed a issue with the Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools that caused a small minority of variants to go unreported under certain conditions expected to arise rarely.
  • Fixed an issue where domain annotations added by the Pfam Domain Search tool started one amino acid later than expected. The corresponding start position in the table produced by the tool was correct.
  • Fixed an issue where the RNA-Seq Analysis tool would sometimes generate TE tracks that could not be used in downstream tools. The error occurred when the "Calculate expression for genes without transcripts" option was used on a gene track where two genes had the same name, one of the genes contained the other, and neither gene had a transcript.
  • Fixed an issue where the RNA-Seq Analysis tool would show an error if the first chromosome or contig contained no transcripts and the "Calculate expression for genes without transcripts" option was used.
  • Fixed a concurrency bug in the Copy Number Variant Detection tool, which very rarely resulted in the tool reporting all low-coverage targets on one or more chromosomes as false positive deletions. (Biomedical enabled Genomics Server only)
Compatibility

The following are the corresponding clients for the QIAGEN CLC Genomics Server 9.1.3:

  • QIAGEN CLC Genomics Workbench 10.1.3
  • Biomedical Genomics Workbench 4.1.3
  • QIAGEN CLC Command Line Tools 4.1.3

We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 10.0.0, 10.0.1 10.1, 10.1.1 and 10.1.2, Biomedical Genomics Workbench 4.0, 4.1, 4.1.1 and 4.1.2, and CLC Command Line Tools 4.0, 4.1, 4.1.1 and 4.1.2 can also connect to QIAGEN CLC Genomics Server 9.1.3. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

Advanced notice

SOLiD colorspace data support, including import, will not be available from QIAGEN CLC Genomics Server 11.0 onwards.

CLC Server Command Line Tools

This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 9.1.3.

Compatibility

CLC Command Line Tools 4.1.3 is the corresponding client for QIAGEN CLC Genomics Server 9.1.3.

CLC Command Line Tools 4.1.3 can also act as a client for the QIAGEN CLC Genomics Server 9.1.2, 9.1.1, 9.1 and 9.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.



QIAGEN CLC Genomics Server 9.1.2

Release date: 2017-12-05

Shared with workbenches

Changes and bug fixes

  • Fixed an issue with the mapping tool in the QIAGEN CLC Genomics Server, which is used in tools involving a mapping stage, such as Map Reads to References, Map Reads to Contigs and RNA-Seq Analysis, where length and similarity fraction cut-offs in some cases were ignored for reads longer than 500bp.
  • Fixed a bug in the Amino Acid Changes tool, and in Bx-enabled servers, the Add Information about Amino Acid Changes tool, where the CDS reference was used instead of the RNA reference when annotating coding region changes if the RNA and CDS annotations could not be matched. This could result in variants in UTR regions not being reported. The matching has been improved by supporting the 'parent' field used by the GFF3 file format to pair CDS and RNA references.
  • Fixed an issue where the number of input samples to the Map Reads to Reference tool and Map Reads to Contigs tools would be silently limited to 120. The execution is now aborted with a warning message. Each analysis must be started with 120 samples maximum.
  • Fixed a bug in the RNA-Seq Analysis tool where, when run in "Genes and transcripts" mode, and using "Total counts" as Expression value, the expression values reported for GE tracks would not include shared exon counts. Downstream analyses based on the Set Up Experiment tool could be affected by this issue. Using affected GE tracks as input to the following tools would *not* affect their results: Differential Expression for RNA-Seq, Create Heat Map for RNA-Seq and PCA for RNA-Seq.
  • The behavior of the RNA-Seq Analysis tool has been changed when the option “Genome annotated with genes and transcripts” is used together with the option “Calculate expression for genes without transcripts".
    • The counts of genes without transcripts are calculated. Previously only the TPM and RPKM were calculated.
    • For a gene without a corresponding transcript, where that gene is overlapped by the intron of another gene, reads aligning to this region are counted towards the expression of the gene without the transcript. Previously such reads were counted as belonging to the intronic region of the overlapping gene.
    • A single-exon transcript for each gene without transcripts is now added to the output TE track.
  • Fixed a an issues with the InDels and Structural Variants tool duplicate breakpoints and variants were reported if reads mapping as broken pairs were included in the analysis.
  • Fixed an issue with the InDels and Structural Variants that caused it to crash if it encountered a particular set of conditions relating to reads with deletions.
  • Fixed an issue where the Low Frequency Variant Detection tool could return NaN for the Probability value in rare instances for small datasets.
  • Compatibility

    The following are the corresponding clients for the QIAGEN CLC Genomics Server 9.1.2

    • QIAGEN CLC Genomics Workbench 10.1.2
    • Biomedical Genomics Workbench 4.1.2
    • CLC Command Line Tools 4.1.2

    We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 10.0.0, 10.0.1 10.1, and 10.1.1, Biomedical Genomics Workbench 4.0, 4.1 and 4.1.1, and CLC Command Line Tools 4.0, 4.1 and 4.1.1 can also connect to QIAGEN CLC Genomics Server 9.1.2. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

    Advanced notice

    Support for SOLiD colorspace data will be phased out over the next 12 months.  If you are concerned about the proposed change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).

    CLC Server Command Line Tools

    This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 9.1.2.

    Compatibility

    CLC Command Line Tools 4.1.2 is the corresponding client for QIAGEN CLC Genomics Server 9.1.2.

    CLC Command Line Tools 4.1.2 can also act as a client for the QIAGEN CLC Genomics Server 9.1.1, 9.1 and 9.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.



    QIAGEN CLC Genomics Server 9.1.1

    Release date: 2017-06-22

    Bug fixes

    • Fixed an issue introduced in QIAGEN CLC Genomics Server 8.5 causing the Merge Annotation Tracks tool to fail when used on tracks with more than 6 chromosomes.
    • Fixed an issue introduced in the Biomedical enabled QIAGEN CLC Genomics Server 9.1 where workflows containing the Copy Number Variant Detection tool could not be updated automatically. (Biomedical-enabled servers only)

    Compatibility

    The following are the corresponding clients for the QIAGEN CLC Genomics Server 9.1.1

    • QIAGEN CLC Genomics Workbench 10.1.1
    • Biomedical Genomics Workbench 4.1.1
    • CLC Command Line Tools 4.1.1

    We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 10.0.0, 10.0.1 and 10.1, Biomedical Genomics Workbench 4.0 and 4.1, and QIAGEN CLC Command Line Tools 4.0 and 4.1 can connect to QIAGEN CLC Genomics Server 9.1.1. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

    Advanced notice

    • Support for SOLiD colorspace data will be phased out over the next 18 months.  If you are concerned about the proposed change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).
       

    QIAGEN CLC Server Command Line Tools

    This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 9.1.1.

    Compatibility

    CLC Command Line Tools 4.1.1 is the corresponding client for QIAGEN CLC Genomics Server 9.1.1.

    CLC Command Line Tools 4.1.1 can also act as a client for the QIAGEN CLC Genomics Server 9.1 and 9.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.



    QIAGEN CLC Genomics Server 9.1.0

    Release date: 2017-06-15

    Server specific

    • Improved messaging in the web administrative interface when workflows installed on the server have unresolved dependencies, such as missing plugins, licenses or data.
    • More detailed feedback is now presented in the Plugins tab of the web administrative client when there are issues with installed plugins, such as missing or expired licenses or version incompatibilities.
    • Fixed a connection issue with LDAP authentication over SSL when the "Disable SSL certificate check" setting was used. This problem was introduced in QIAGEN CLC Genomics Server 9.0.

    Shared with workbenches

    Improvements

    • When importing tracks, the history of the track now contains the full path name of the imported file.

    Bug fixes

    • Fixed an issue with the Basic Variant DetectionLow Frequency Variant Detection and Fixed Ploidy Variant Detection tools that could cause the count and frequency values to be too low for a small subset of those variants that are contained within a larger variant region (e.g. an MNV or deletion). For a variant to be affected by this problem, there needed to be at least two other potential variants nearby that were disregarded during the variant calling process. This circumstance and our testing suggest this is a rare issue.
    • Fixed a bug that in some cases would result in incorrect BaseQRankSum values being reported in the outputs of the Basic Variant DetectionLow Frequency Variant Detection and Fixed Ploidy Variant Detection tools.
    • Fixed an issue where the GFF3 Exporter could generate invalid GFF3 for features of length 0.

    Shared with Biomedical enabled Genomics Server only

    • Fixed a bug in the Copy Number Variation Detection tool where the target-level output could not be produced unless a gene track was also specified.
    • Fixed an issue in the Copy Number Variation Detection tool where the data in the "Fold-change (adjusted)" and "Fold-change (raw)" columns were reversed in the target-level CNV output.

    Compatibility

    The following are the corresponding clients for the QIAGEN CLC Genomics Server 9.1.0

    • QIAGEN CLC Genomics Workbench 10.1.0
    • Biomedical Genomics Workbench 4.1.0
    • CLC Command Line Tools 4.1.0

    We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 10.0.0 and 10.0.1, Biomedical Genomics Workbench 4.0, and CLC Command Line Tools 4.0 can connect to QIAGEN CLC Genomics Server 9.1.0. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

    Advanced notice

    • Support for SOLiD colorspace data will be phased out over the next 18 months.  If you are concerned about the proposed change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).
     

    QIAGEN CLC Server Command Line Tools

    This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 9.1.0

    Compatibility

    CLC Command Line Tools 4.1.0 is the corresponding client for QIAGEN CLC Genomics Server 9.1.0.

    CLC Command Line Tools 4.1.0 can also act as a client for the QIAGEN CLC Genomics Server 9.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.



    QIAGEN CLC Genomics Server 9.0

    Release date: 2017-03-02

    Server specific

    New features and improvements

    • The tabs "Import", "Export" and "Sequence Text" have been removed from the web administration interface. Viewing, import and export functionality are available via Workbench clients, and import and export functionality is also available using the CLC Command Line Tools client.
    • The mapping tool in the Workbench, which is used in tools involving a mapping stage, such as  Map Reads to References,  Map Reads to Contigs and RNA-Seq Analysis has been updated. The update includes improved read mapping quality and speed (especially for longer reads), improved memory performance for the index building stage, and various minor bug fixes. The new mapping tool corresponds to the clc_mapper tool included in Assembly Cell 5.0.3, planned for release in March, 2017.
    • Temporary *.cpw files are now deleted immediately after installation of server workflows from the workbench. Previously these were deleted later, when the finished server process for the installation was removed.
    • Various minor improvements

    Bug fixes

    • Fixed a problem where permission changes were not applied as expected when using the  "Apply to all subfolders" option when setting group permissions on a folder in server data locations.
    • Fixed an issue where the QIAGEN CLC Genomics Server would wait indefinitely when there was a stalled connection to the LDAP server.
    • Fixed an issue that caused the import of Wiggle and USCS chromosome band files to fail on QIAGEN CLC Genomics Server setups.
    • Fixed an issue where batch jobs submitted to the QIAGEN CLC Genomics Server would not always display all the sub-processes in the Processes tab in a Workbench.
    • Various minor bugfixes.

    Shared with workbenches

    New tools for RNA-Seq

    • Create Combined RNA-Seq Report - makes it possible to join multiple reports generated by the RNA-Seq Analysis tool into one combined overview report.
    • PCA for RNA-Seq*  - clusters samples in 2D or 3D. Known metadata about each sample is added as an overlay.
    • Differential Expression for RNA-Seq*  - uses multi-factorial statistics based on a negative binomial GLM.
    • Create Heat Map for RNA-Seq* - simultaneously clusters samples and features. Known metadata about each sample is added as an overlay.*
    • Create Expression Browser* - allows expression values, statistical results, and gene annotations to be viewed together.*
    • Create Venn Diagram for RNA-Seq* - shows differentially expressed genes shared between experimental conditions.*
    • Gene Set Test - tests the output from the Differential Expression for RNA-Seq tool for overrepresented gene sets (such as Gene Ontology terms) using a hypergeometric test.
    • Import | RNA Spike-ins - for importing RNA spike-in sequences and concentration data.

    *Tools marked with an asterisk were available to earlier Workbench versions via the Advanced RNA-Seq plugin.

    These tools automatically account for differences due to sequencing depth, removing the need to normalize input data. They work with existing RNA-seq TE and GE tracks. Changes made in this release mean that outputs from the Differential Expression for RNA-Seq tool can now be used as inputs to the Extract Annotations (for QIAGEN CLC Genomics Server)  and Extract Reads Based on Overlap tools.

    RNA-Seq Analysis

    • The RNA-Seq Analysis tool now supports RNA spike-ins, such as ERCC and SIRV, for quality control. This makes it possible to validate RNA-Seq experiments by comparing known spike-in concentrations to measured transcript concentrations. Spike-ins can be imported using the new RNA Spike-ins Import tool.
    • The RNA-Seq Analysis report has been revised and updated:
      • We now show the distribution of the biotypes that the reads mapped to.
      • The strand specificity  of the mapped reads is now reported.
      • Transcript coverage plots make it possible to detect and visualize 5' and 3' coverage bias.
      • For paired-end reads, we now detect and warn about potential adapter read-through.
    • A biotype column is now available in the Expression Track tables produced by the RNA-Seq Analysis tool, when biotype information is available.
    • The Mapping options of the RNA-Seq Analysis tool, "Map to gene regions only" and "Also map to inter-genic regions", have been removed. The tool now runs by mapping reads to the full reference supplied, which is equivalent to choosing the recommended "Also map to inter-genic regions" option in earlier versions.
    • The RNA-Seq Analysis tool now always uses the "Expression level" option "Use EM estimation (recommended)" to quantify expression. This is more accurate than the previous default option. Differences are especially noticeable for Transcript Expression (TE) tracks.
    • The RNA-Seq Analysis quantification by EM estimation now runs faster.
    • In RNA-Seq analyses, reads that map uniquely to a genome position are now always marked as unique. Previously, a uniquely mapped read would be marked as ambiguous if it mapped to a position with multiple overlapping genes.
    • Exon IDs will no longer be included in the ENSEMBL column of transcript expression (TE) tracks generated by the RNA-Seq Analysis tool. Gene and transcript names will continue to be listed in this column.

    Import/Export

    • A tool to import PacBio data is now available. It is located at Import | PacBio  in Workbenches.
    • The GFF2/GTF/GVF tracks importer can no longer be used to import GFF3 format files. The new GFF3 tracks importer should be used for this instead.
    • The GFF3 importer has been updated with respect to the handling of CDS features. In earlier versions, CDSs with different IDs but the same parent gene would always be merged into the same CDS feature during import. This behavior will still occur in cases where all CDSs in the GFF3 file either have unique IDs or no IDs. For GFF3 files where there are any CDSs with identical IDs, then only CDSs with the same ID are merged into a single feature.
    • The Import | Tracks tool now accepts files with a .fna extension.
    • The speed of importing to tracks where the original file contains data relating to many chromosomes has been substantially improved.
    • The Cosmic option of  the Import | Tracks tool is now more flexible with regards to the column headings in the files being imported.
    • An exporter has been added to export annotations on sequences or tracks to Generic Feature Format Version 3 (GFF3) format.
    • An option has been added to create an index file when exporting to BAM format.

    New features and improvements

    • Toolbox rearrangement: the expression analysis tools are now in two top-level folders: "RNA-Seq Analysis" and "Microarray and Small RNA Analysis". The former top level Toolbox folder Transcriptomics Analysis has been removed.
    • When working with Gene Sets that refer to Gene Ontology terms, gene annotations are now automatically propagated to parent Gene Ontology terms.  This improvement affects the tools Hypergeometric Tests on Annotations and Gene Set Enrichment Analysis (GSEA).
    • The mapping tool used as part of Map Reads to References and the Map Reads to Contigs tools has been updated. The update includes improved read mapping quality for longer reads, improved memory performance for the index building stage, as well as various minor bug fixes. The new mapping tool corresponds to the clc_mapper tool included in Assembly Cell 5.0.3, planned for release in March, 2017.
    • The default value for the parameter "Maximum guidance-variant length" in the tool Local Realignment tool has been changed to 200 (was 100). This change applies to all ready-to-use workflows and when the tools is launched directly.
    • The Basic Variant Detection tool will no longer report N as an alternative allele when there is an ambiguous base at a variant position.
    • The report generated by the tool Create Statistics for Target Regions now includes a "≥" sign instead of a ">" sign.
    • The "Additional Reporting" options in the Create Sequencing QC Report tool,  "Quality analysis" and "Over-representation analysis" have been removed. These outputs are now generated by default.
    • Options to search the full text or abstracts available in Pubmed have been added to the Search for Reads in SRA tool
    • Support has been added for 'negative lookahead' when using Java regular expressions when using the Motif Search Tool.
    • For new or existing sequence lists the sequencing platform can now be specified via the Read Group setting of the Element Info view.
    • The speed of searches for data elements with associations to specified metadata, from within a Metadata Table, has been greatly improved. To enable metadata related searches to work after upgrading to the QIAGEN CLC Genomics Server 9.0, indices for the locations containing the relevant data will need to be rebuilt.
    • Various minor improvements

    Bug fixes and changes

    • Fixed an issue where the index building stage of the Map Reads to References and the Map Reads to Contigs tools was not taking into account the maxcores setting in the cpu.properties file, where this had been configured.
    • Fixed an issue where sequence circularity was not reported in the output from the Map Reads to References tool.
    • Fixed a bug in the Create Detailed Mapping Report, which sometimes reported incorrect read counts for circular sequences.
    • Fixed an issue where the Basic Variant DetectionLow Frequency Variant Detection and  Fixed Ploidy Variant Detection tools reported homozygous reference insertions in cases where a heterozygous variant was possible but the insertion variant was disregarded during filtering.
    • Fixed an issue where the Identify Known Mutations from Sample Mappings tool would fail if it was part of a workflow and it received multiple input sample mappings as input.
    • Fixed an issue with GenBank and EMBL exports where quoting specifications were not being conformed to.
    • Fixed an issue where a workflow containing an export step that failed did not provide any indication that a problem had occurred.
    • The speed of sorting and loading tracks in the Workbenches has been greatly improved. Due to these changes, tracks created with this version of the QIAGEN CLC Genomics Server and later ones cannot be used in older Workbenches or Servers. Backwards compatibility has been maintained: tracks created using older versions of the Workbench or QIAGEN CLC Genomics Server can continue to be used.
    • Various minor bugfixes.
    Shared with Biomedical enabled Genomics Server only
    • Two new human reference data sets are available for download from the Reference Data Manager. One is based on Ensembl 86 and the other is based on RefSeq GRCh38.p9.
    • The three workflows Identify and Annotate Differentially Expressed Genes and Pathways for human, mouse, and rat have been replaced by three new workflows of the same names. The new workflows benefit from the inclusion of new RNA-seq tools.
    • The Ready-to-use workflows listed under the "Whole Transcriptome Sequencing" folder of the Workbench Toolbox now support strand-specific RNA-seq protocols by allowing the "Strand Specific" parameter to be set.
    • In all Ready-to-Use workflows containing the tool Map Reads to Reference, the default value for the parameter "Cost of insertions and deletions" has been changed to "affine" (it used to be "linear"). Default values have not been changed in the case where the tool is launched directly.
    • Less temporary space is now consumed when downloading data via the Reference Data Manager.
    • When working with Gene Sets that refer to Gene Ontology terms, gene annotations are now automatically propagated to parent Gene Ontology terms.  This improvement affects the tool Identify Differentially Expressed Gene Groups and Pathways.
    • Fixed a bug in the Create Detailed Mapping Report (or QC for Read Mapping tool in Biomedical enabled Genomics Server), which sometimes reported incorrect read counts for circular sequences.
    Retirement
    • The GFF exporter has been retired and is no longer available. The new GFF3 exporter should be used instead.
    • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools have been retired.
    • The tool Trim Primers of Mapped Reads has been retired. For trimming primers from mapped reads, please use the Trim Primers and their Dimers from Mapping tool, which is distributed with the QIAGEN GeneRead Panel Analysis Server Plugin.
    Compatibility

    The follow software are the corresponding clients for the QIAGEN CLC Genomics Server 9.0

    • QIAGEN CLC Genomics Workbench 10.0
    • Biomedical Genomics Workbench 4.0 (when the server has the Biomedical Extension)
    • CLC Command Line Tools 4.0

    Plugin notes

    • The Advanced RNA-Seq plugin has been retired. The tools from this plugin have been integrated into the software. Please see the New Tools section for more details.

    QIAGEN CLC Server Command Line Tools

    All QIAGEN CLC Genomics Servers

    New Tools
    • create_combined_rnaseq_report        Create Combined RNA-Seq Report
    • create_expression_browser               Create Expression Browser
    • create_heatmap_for_rnaseq              Create Heatmap fo RNA-Seq
    • create_venn_diagram_for_rnaseq     Create Venn Diagram for RNA-Seq
    • differential_expression_rna_seq        Differential Expression for RNA-Seq
    • gene_set_test                                    Gene Set Test
    • principal_component_for_rna_seq     PCA for RNA-Seq
    • spikein_control_import                       RNA Spike-ins
    Other tools
    • -e gff3     export to gff3 format
    Improvements
    • Help for the CLC Command Line Tool is no longer printed to the console when errors are returned.

    Changes

    Commands removed
    • probabilistic_variant_detection       Probabilistic Variant Detection. Legacy tool, now retired.
    • quality-based_variant_detection     Quality based Variant Detection. Legacy tool, now retired.
    • -e gff     export to gff.  Use the new gff3 exporter instead.

    rna_seq

    • --spike-in-settings                        Map reads to spike-in controls (default: NONE)
    • --spikein-controls                          Select spike-in controls

    exporting to bam format  (-A export -e bam)

    • --index <Boolean>                        >Create an index file (.bai) (default: false)
    Options removed from commands

    rna_seq

    • --em-enabled
    • --mapping-type

    The tool now runs with EM enabled by default.

    sequencing_qc_report

    • --include-overrepresentation-analysis
    • --include-quality-score-analysis

    The tool now generates these outputs as part of the report by default.

    Biomedical Enabled QIAGEN CLC Genomics Servers only

    Changes in addition to those listed for all QIAGEN CLC Genomics Servers
    Options removed from commands

    qc_for_sequencing_reads

    • --include-overrepresentation-analysis
    • --include-quality-score-analysis


    QIAGEN CLC Genomics Server 8.5.5

    Release date: 2017-06-08

    Server specific

    • Fixed an issue that caused the import of Wiggle and USCS chromosome band files to fail on QIAGEN CLC Genomics Server setups.
    • More detailed feedback is now presented in the Plugins tab of the web administrative client when there are issues with installed plugins, such as missing or expired licenses or version incompatibility.

    Shared with workbenches

    Improvements

    • When importing tracks, the history of the track now contains the full path name of the imported file.

    Bug fixes

    Compatibility

    • QIAGEN  QIAGEN CLC Genomics Workbench 9.5.5 is the corresponding client for QIAGEN  QIAGEN CLC Genomics Server 8.5.5.
    • Biomedical Genomics Workbench 3.5.5  is the corresponding client for QIAGEN  QIAGEN CLC Genomics Server 8.5.5.
    • CLC Command Line Tools 3.5.5 is the corresponding client for QIAGEN  QIAGEN CLC Genomics Server 8.5.5.

    We recommend running the corresponding versions of clients for QIAGEN  QIAGEN CLC Genomics Server. However, QIAGEN  QIAGEN CLC Genomics Workbench 9.5.4, 9.5.3, 9.5.2, 9.5.1, 9.5, 9.0.1 and 9.0, Biomedical Genomics Workbench 3.5.4, 3.5.3, 3,5.2, 3.5.1, 3.5, 3.0.1 and 3.0, and CLC Command Line Tools 3.5.4, 3.5.3, 3.5.2, 3.5.1, 3.5, 3.0.1 and 3.0 can connect to QIAGEN CLC Genomics Server 8.5.5. In addition, QIAGEN  QIAGEN CLC Genomics Workbench 9.5.x and Biomedical Genomics Workbench 3.5.x and CLC Command Line Tools 3.5.x can  connect to a QIAGEN  QIAGEN CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

     

    QIAGEN  CLC Server Command Line Tools

    This is a compatibility release to supply the corresponding client for QIAGEN  QIAGEN CLC Genomics Server 8.5.5.

    Compatibility

    CLC Command Line Tools 3.5.5 is the corresponding client for QIAGEN  QIAGEN CLC Genomics Server 8.5.5.

    CLC Command Line Tools 3.5.5 can also act as a client for the QIAGEN  QIAGEN CLC Genomics Server 8.5.4, 8.5.3, 8.5.2, 8.5.1, 8.5., 8.0.1 and 8.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN  QIAGEN CLC Genomics Server.



    QIAGEN CLC Genomics Server 8.5.4

    Release date: 2017-02-14

    Bug fixes

    • A timeout value that would lead a job to fail after 24 hours, which was introduced as part of optimizations to run on multiple threads in the QIAGEN CLC Genomics Server 8.5 has been extended to 7 weeks. The tools affected are Annotate from Known Variants, Filter against Known Variants, Filter against Control Reads, Annotate with Exon Number, Annotate with Flanking Sequences, Filter Marginal Variant Calls, Compare Sample Variant Tracks, Trio Analysis, GO enrichment Analysis, Amino Acid Changes, Annotate with Conservation Score, Predict Splice Site Effect, Link Variants to 3D Protein Structure, Merge Annotation Tracks, Create Statistics for Target Regions, Fisher Exact Test, Annotate with Overlap Information, Filter Based on Overlap, Filter Reference Variants, Identify Candidate Variants, Coverage Analysis, and InDels and Structural Variants.
    • Fixed an issue in the RNA-Seq Analysis tool where running in EM mode, with a "Strand specific" setting of "Forward" or "Reverse" would result in the second read of a pair mapped as a broken pair being counted incorrectly if that read was mapped outside a region annotated as a transcript.
    • Fixed an issue where an error arose when using the RNA-Seq Analysis tool with the EM option and a strand specific setting of "Forward" or "Reverse" in cases where the second read of mapped broken pair mapped to the opposite strand of the strand specific setting.
    • Fixed an issue with the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools where the forward and/or reverse count for a longer variant, supported by paired reads with both children having the same direction, could be too low. The forward count and reverse count is now reported correctly.
    • Fixed an issue with the InDels and Structural Variants tool where an incorrect insertion could be called when the optimal alignment of a read's unaligned end around the breakpoint included a gap in the insertion sequence.
    • Fixed an issue in the InDels and Structural Variants tool that would terminate analysis of large read mappings prematurely a fraction of the times.
    • Fixed an issue with the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools where the count and read count could be reported as marginally higher than they actually were in a small minority of cases. For the affected variants, this could then also result in variant frequencies being reported that were slightly higher than they should have been, in some cases above 100%. Variants affected by this issue are a small subset of variants where the variant affected overlapped another potential variant and where only the affected variant was then reported. This change could lead to a small decrease in the number variants reported compared to earlier versions of the CLC software, due to a variant no longer passing the count or read count filtering constraints. The impact of this change is expected to be low. For example, in our tests, for a particular analysis that reported 250,000 variants, 30 fewer were reported with the same parameters and filters applied after this fix was implemented.
    • Fixed an issue where the Basic Variant Detection, Fixed Ploidy Variant Detection, Low Frequent Variant Detection and Local Realignment tools could fail if a deletion was encountered at the end of a match between a read and the reference in the mapping used as input.
    • Fixed an issue in the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequent Variant Detection tools where the tools could stop with an error. The problem arose when a read split up within a mapping (e.g. to map to separate exons) was split into 4 or more parts, and at least 4 of those parts would map within a region of adjacent variants being considered as a possible multiple nucleotide variant (MNV). This infrequent problem was most likely to occur when using high coverage RNA-Seq mappings and looking for variants occurring at low frequency. It was introduced in the previous bugfix release of the QIAGEN CLC Genomics Server, version 8.5.3.

    Specific to Biomedical enabled Genomics Server

    • A timeout value that would lead a job to fail after 24 hours, which was introduced as part of optimizations to run on multiple threads in the QIAGEN CLC Genomics Server 8.5 has been extended to 7 weeks. The tools affected are Add Information from Variant Databases, Remove Variants Found in External Database, Remove Germline Variants, Add Exon Number, Add Flanking Region, Remove False Positives, Identify highly Mutated Gene Groups and Pathways, Add Information About Amino Acid Changes, Add Conservation Scores, Identify Variants with Effect on Splicing, Link Variants to 3D Protein Structure, QC for Targeted Sequencing, Identify Enriched Variants in Case vs Control Samples, Add Information from Overlapping Genes, Add information from Genomic Regions, Add Information from Overlapping Variants, Remove Variants Outside Genome Genome Regions, Remove Variants Outside Target Regions, Remove Variants Inside Genome Regions, Identify Mutated Genes, Remove Reference Variants, and Whole Genome Coverage Analysis.

    Compatibility

    • QIAGEN CLC Genomics Workbench 9.5.4 is the corresponding client for QIAGEN CLC Genomics Server 8.5.4.
    • Biomedical Genomics Workbench 3.5.4  is the corresponding client for QIAGEN CLC Genomics Server 8.5.4.
    • CLC Command Line Tools 3.5.4 is the corresponding client for QIAGEN CLC Genomics Server 8.5.4.

    We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 9.5.3, 9.5.2, 9.5.1, 9.5, 9.0.1 and 9.0, Biomedical Genomics Workbench 3.5.3, 3,5.2, 3.5.1, 3.5, 3.0.1 and 3.0, and CLC Command Line Tools 3.5.3, 3.5.2, 3.5.1, 3.5, 3.0.1 and 3.0 can connect to QIAGEN CLC Genomics Server 8.5.4. In addition, QIAGEN CLC Genomics Workbench 9.5.x and Biomedical Genomics Workbench 3.5.x and CLC Command Line Tools 3.5.x can  connect to a QIAGEN CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

     

    Advanced notice

    • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in March, 2017.
    • The Expression Profiling by Tags tools (Extract and Count Tags, Create Virtual Tag List, and Annotate Tag Experiment) are scheduled to be removed from the Server and Workbench in March, 2017.
    • Support for some older operating systems (OS), listed below, will be discontinued in March, 2017. Software released at that time and later may still run without issue, but problems experienced due to using an unsupported OS will not be addressed. If you are concerned about the proposed change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com), letting them know the OS being used and the products you are running on that OS.
      • Windows: Windows Vista and Windows Server 2008
      • Mac: Mac OS X 10.7 and 10.8
      • Linux:  Red Hat Enterprise Linux 5, SUSE Linux Enterprise Server 10 and 11 and Fedora 6 through 21

    QIAGEN CLC Server Command Line Tools

    This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 8.5.4.

    Compatibility

    CLC Command Line Tools 3.5.4 is the corresponding client for QIAGEN CLC Genomics Server 8.5.4.

    CLC Command Line Tools 3.5.4 can also act as a client for the QIAGEN CLC Genomics Server 8.5.3, 8.5.2, 8.5.1, 8.5., 8.0.1 and 8.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.



    QIAGEN CLC Genomics Server 8.5.3

    Release date: 2016-12-14

    Bugfixes and Improvements

    For the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection tools, the following have been addressed:

    • Fixed an issue where the coverage of a longer variant that contained another variant was reported for both the longer variant and the contained variant. The coverage for the contained variant is now reported correctly.
    • Fixed an issue affecting coverage calculation for SNVs without immediately adjacent variants when using paired read data: if the second read of a pair containing the variant did not meet the requirements of the quality filter, neither the first nor second read of that pair contributed to the coverage calculated for the variant.
    • Fixed an issue where, for an SNV without immediately adjacent variants, overlapping reads of a pair that had conflicting base calls for that variant position contributed to the values calculated for coverage, read coverage, and read count of that variant.
    • Fixed a bug where count, read count, and forward- and reverse read count could be incorrect for variants found in overlapping regions of a pair of reads and where the variant was originally identified as being adjacent to one or more other variants.

    The above issues, including information on the products affected, are described on the public notification page: Coverage and count reporting for variants in certain circumstances are incorrect

    For the Identify Known Mutations from Sample Mappings tool, the following issues have been addressed:

    • Fixed an issue with the Identify Known Mutations from Sample Mappings tool where reads in a sample mapping were not identified as supporting the presence of a known variant in cases where the first position of the variant region in the mapped read contained a gap.
    • Fixed an issue with the Identify Known Mutations from Sample Mappings tool where a read containing a variant longer than a known variant being tested for was counted as supporting the known variant in cases where the first part of the read’s variant sequence is identical to that of the known variant.
    • Fixed an issue in the Identify Known Mutations from Sample Mappings tool where overlapping reads of a pair having conflicting base calls for a variant position could contribute to the coverage calculated for that variant.

    Compatibility

    • QIAGEN CLC Genomics Workbench 9.5.3 is the corresponding client for QIAGEN CLC Genomics Server 8.5.3.
    • Biomedical Genomics Workbench 3.5.3  is the corresponding client for QIAGEN CLC Genomics Server 8.5.3.
    • CLC Command Line Tools 3.5.3 is the corresponding client for QIAGEN CLC Genomics Server 8.5.3.

    We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 9.5.2, 9.5.1, 9.5, 9.0.1 and 9.0, Biomedical Genomics Workbench 3,5.2, 3.5.1, 3.5, 3.0.1 and 3.0, and CLC Command Line Tools 3.5.2, 3.5.1, 3.5, 3.0.1 and 3.0 can connect to QIAGEN CLC Genomics Server 8.5.3. In addition, QIAGEN CLC Genomics Workbench 9.5.x and Biomedical Genomics Workbench 3.5.x and CLC Command Line Tools 3.5.x can  connect to a QIAGEN CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

    Advanced notice

    • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in early 2017.
    • The Expression Profiling by Tags tools (Extract and Count Tags, Create Virtual Tag List, and Annotate Tag Experiment) are scheduled to be removed from the Server and Workbench in spring, 2017.
    • Support for some older operating systems (OS), listed below, will be discontinued in early 2017. Software released at that time and later may still run without issue, but problems experienced due to using an unsupported OS will not be addressed. If you are concerned about the proposed change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com), letting them know the OS being used and the products you are running on that OS.
      • Windows: Windows Vista and Windows Server 2008
      • Mac: Mac OS X 10.7 and 10.8
      • Linux:  Red Hat Enterprise Linux 5, SUSE Linux Enterprise Server 10 and 11 and Fedora 6 through 21

    QIAGEN CLC Server Command Line Tools

    This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 8.5.3.

    Compatibility

    CLC Command Line Tools 3.5.3 is the corresponding client for QIAGEN CLC Genomics Server 8.5.3.

    CLC Command Line Tools 3.5.3 can also act as a client for the QIAGEN CLC Genomics Server 8.5.2, 8.5.1, 8.5., 8.0.1 and 8.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.

     


    QIAGEN CLC Genomics Server 4.0

    Release date: 2012-02-13

    New plug-ins and plug-in updates

    • Genomics Gateway plug-in updated
      • New tools for analyzing variants in groups of samples, enabling systematic analysis of genetic variants for whole genome, exome or targeted approaches.
        • Find Common Variations in Group. This can be used to find common variants in a group of variant tracks.
        • Fisher Exact Test. Comparing two groups of variant tracks (e.g. can be used for case-control studies). You can see which variants are found more common in the case compared to the control group using the Fisher Exact test.
        • Filter against Control Reads. This can be used to compare a single case variant track against a negative control from the same sample. It will check whether a certain number of the reads in the control sample have the same allele present as in the case variant.
      • New tools for functional annotation of variants
        • Go Enrichment Analysis for identifying significant gene ontology terms, which are annotated to genes having at least one variation.
        • Annotation with Conservation Scores. By importing a conservation score track (e.g. PhyloP Scores), variants can be annotated with a conservation score. Variants with a high score are assumed to alter functionally important regions.
      • New data structure.
        • All tracks are now saved as single files, and you can create a Track List to visualize them together.
        • A tool is available for data conversion from track sets to single tracks
      • New organization of the “Tool box” to provide a better overview
      • Support for batching and running tools on a Genomics Server
      • The Track List view supports drag and drop for adding and re-arranging tracks
      • Several Graph tracks can be created and displayed
      • Read the updated manual here.
    • Probabilistic Variant Detection Plug-in updated
      • The probability used as threshold for the algorithm is now reported in the output
      • Variants reported cDNA-level numbering and variant information compatible with www.hgvs.org/

    Core server features and improvements

    • Possibility to import data from the Workbench on the Server. This was previously only possible with NGS data import.
    • BLAST database management: It is now possible to delete BLAST databases in the Web interface.
    • The blue dot indicating that a tool could be run on the server has been removed in order to provide a simpler user interface for new users.
    • External Applications: parameters for maximum number of cores and the name of the user logged in can be automatically provided by the server when the algorithm is executed.
    • Support for redirecting non-SSL port to SSL port when accessing the server’s web interface.
    • Command Line Tools: it is allowed to provide CLC urls with full path including the .clc file extension.

    Algorithm features and improvements

    • New de novo assembler.
      • Scaffolding is integrated into the assembly. This means better resolution of contigs and insertion of Ns when two contigs cannot be joined in sequence but there is pair information that connects them.
      • New extended report for the assembly with information about nucleotide distribution, contig lengths measurements and scaffolding regions.
      • New parameter for specifying the maximum bubble size. There is a default value which is automatically calculated based on the input data.
      • New white paper with benchmarks and results from quality control.
      • The old de novo assembler is available as a plug-in. At the end of 2012, the plug-in will be discontinued, so it should only be used for backwards compatibility with results from older runs or if the new assembler fails.
    • SNP and DIP detection results include cDNA-level numbering and variant information compatible with www.hgvs.org/
    • SAM files exported from the Server now include basic information about read groups. Furthermore, read orientation for paired reads is now preserved when exporting to SAM and BAM files.
    • Improved exploitation of multi-core machines in read-mapping, RNA-Seq, and de-novo assembly.
    • Improved performance and memory management for high-throughput analyses in general.

    Bug fixes

    • Export of BLAST results was not possible on the server.


    QIAGEN CLC Genomics Server 3.6

    Release date: 2011-11-29

    New plug-ins and plug-in updates

    • New plug-in released: Ab Initio Transcript Discovery
      • Large gap mapper plug-in is renamed and now includes a tool for transcript discovery. Based on gapped alignments of RNA-Seq data, the plug-in identifies new transcripts and creates or extends annotations on the reference sequence that can be used for measuring gene expression using the RNA-Seq Analysis tool of the Genomics Workbench. The plug-in provides functionality a la Cufflinks/TopHat.
    • Genomics Gateway plug-in updated
      • New refiner: variant frequency. This allows you to filter a variation track, so that only the variants that have a frequency above a user-defined threshold remain. Note that the filter only applies to the frequency of non-reference alleles.
      • Performance improvements when visualizing read tracks
      • Fixed: CDS annotations from Ensembl did not include start codons
      • Fixed: Some variation tracks were not always recognized as variations. This means that the variation-specific refiners could not be used.
      • Fixed: Table view of annotation tracks could have a very large number of columns that are now combined into one column.
      • Fixed: There was an error when closing a view without saving changes. This could lead to subsequent errors when trying to rename tracks.
    • Structural variation plug-in updated
      • Only detection of insertions, deletions and interchromosomal variations are now supported.
      • The plug-in has a problem with repeats. The best way to work around this is to ignore non-specific matches when doing the mapping, to run the structural variant detection with a very stringent p-value cutoff and filter repeats out afterwards if possible (this could be by refinement with the microsatallite track from Biobase or another repeat track using the Genomics Gateway).
      • Integration of exporter to export results in circos format.
    See a list of all plug-ins here. The pdf documentation of all plug-ins has been updated as well.

    Core server features and improvements

    • The grid integration is now released out of beta
      • Core management: you can restrict the maximum number of cores that the Grid Worker is allowed to use. This is useful the execution node is shared with other jobs and the CLC Grid Worker needs to respect an assignment of the number of cores to use. This is mainly an issue for the De novo assembly and Read Mapping algorithms but the restriction applies to all algorithms that use several cores.
    • For Oracle databases: There are now two ways of connecting to an Oracle database. One is the traditional using SID style and the other is using thin-style service name. Existing installations do not need to be changed.

    Algorithm features and improvements

    • BLAST is now available on the server
      • Creation of BLAST databases
      • Running BLAST jobs on the server against either databases on the server file system or temporary “on-the-fly” databases.
    • Process tagged sequences
      • A summary report is now available with an overview of the number of reads per bar code.
      • You can search for barcodes (MIDs) on both strands, supporting new 454 protocol.
    • Find Binding Sites and Create Fragments improved:
      • Can now be run on the server
      • If your template sequence contains ambiguity nucleotides (like N, Y etc), these will no longer count as mismatches when checking your primers. Note that the primer base of course need to be covered by the ambiguity symbol (e.g. a T would still be a mismatch if the template sequence has an R, which means either A or G).
      • Fixed: When using multiple template sequences, the choices to open or annotate a fragment from the fragment table did not work properly. They always applied to the first sequence although the fragment was located on another sequence (as indicated in the table).
    • Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read.
    • Enhancing the nomenclature of reporting amino acid changes in variant detection:
      • p. prefix included
      •  ? used for unknown (rather than non-standard “Unknown”)
      • = used to denote an allele which agrees with the reference sequence (rather than missing entries or entries like Ala45Ala)
      • [...] used around ,-separated lists of changes, each change coming from a different CDS annotation
      • [...];[...] scheme used to separate multiple alleles at same site

    Bug fixes

    • Fixed: Import of SOLiD data failed when multiple sets of paired data was selected.
    • Fixed: Calculation of consensus sequence in read mappings: Sometimes a majority of gaps would be ignored and a base erroneously introduced in the consensus sequence. It occurs when 1) there is no coverage in an initial segment of the reference sequence, and 2) a gap is encountered in the global read alignment. From that point onwards, gap counts are included in the consensus vote, but they are taken from the start of the mapping (where they are all 0), so they are out of sync with associated base counts. High gap counts would then kick in further downstream, possibly making the consensus a gap where it should not be. We recommend checking your mapping results manually if you rely on using the consensus sequence for further analysis.


    QIAGEN CLC Genomics Server 3.5

    Release date: 2011-10-12

    New plug-ins and plug-in updates

    Core server features and improvements

    • Permission control on file system. Previously, this feature was only available for customers with a Bioinformatics Database but now all server customers will be able to specify which users should have access to data on the server. This is done by logging in as admin through the Workbench and setting read and write permissions on folders.
    • SSL. The Server now supports secure connections from clients (either Workbench, Command Line Tools or the web interface)
    • Status icon in Workbench is now showing info on current server connection. Clicking the icon when not logged in will display the log-in dialog.
    • Permissions on server commands: server administrators can decide if certain groups should not be allowed to run certain analyses. This can be controlled also for each external application configuration.
    • Permissions on import/export directories: server administrators can decide if certain groups should not be allowed to access import/export directories
    • Web interface import and export from Import/Export directories on server file system
    • Support for attachments on Grid jobs. This means that you can run Next-Generation Sequencing data imports with data from the client file system when running on a grid. Previously you could only import data from the import/export directories.
    • Command Line Tools include a tool for setting permissions on folders on the server.

    Algorithm features and improvements

    • De novo assembly improvements:
      • Word size can now be manually adjusted
      • When update contigs is not selected, the resulting mapping table will also include contigs where no reads map back. This means that the number of rows in the table will be identical to the number of “Simple contigs” produced by the de novo assembler. Previously contigs with less than two reads mapped back would be omitted from the table.
    • Merge Mapping Results will produce a mapping table when mapping tables are provided as input
    • Mapping tables now include a row for reference sequences where no reads map. This is done to provide consistency of results. Opening such an entry in the table will just open the reference sequence in the table.
    • SNP detection no longer ignores ambiguity bases in the reads. Each ambiguity code is treated as a separate variant; no merging of the possible variants covered by each ambiguity code is attempted (this typically only has an effect when using Sanger sequencing data since standard NGS platforms do not use ambiguity base calls).
    • SAM import and export format is now described in detail in the user manual.

    Bug fixes

    • Fixed: Orientation of SOLiD mate-pair data was not set correctly on import. This meant that the reads were marked as broken pairs after mapping. We strongly recommend all users to re-run the import if using SOLiD mate pair data.
    • Fixed: Experiments tables can now be exported in Excel and csv formats
    • Fixed: If a combination of trim options is used, like quality trim or length trim in addition to adapter trimming on both strands, the reads could end up reverse complemented.
    • Fixed: Import of paired data generated by Illumina Casava 1.8 did not match the pairs correctly. Users are advised to re-import and re-analyze all data imported from Casava 1.8.
    • Fixed: De novo assembly sometimes failed on Mac OS 10.7 Lion.
    • Fixed: Errors for read mappings with the text “premature end of .cas file” have now been fixed. This has only been a problem on Windows.


    QIAGEN CLC Genomics Server 3.2.2

    Release date: 2011-07-14

    Bug fixes

    • Fixed: A cache-related bug which would sometimes result in errors when running large jobs.
    • Fixed: A problem with interpretation of broken pairs on re-import from SAM format files.
    • Added missing Java VM-options to the CLC Grid Worker


    QIAGEN CLC Genomics Server 3.2.1

    Release date: 2011-06-27

    Bug fixes

    • De novo assembly produced empty results
    • Paired distances for read mapping were not recorded correctly in history
    • Adapter trim with Command Line Tools: if multiple adapters were provided, only the first was used
    • Various minor bug-fixes


    QIAGEN CLC Genomics Server 3.2

    Release date: 2011-06-21

    New and improved features

    • External applications is now running on grids
    • Secondary peak calling functionality is now available on the server
    • Import of GFF files is now available on the server
    • The High-throughput Sequencing Data Import Location has been redefined as a more general Import/Export location
    • CLC Server Command Line Tools is now released in a final version
    • Mapping
      • New mapping data format supports multiple alignments and allows for import and full visualization of Complete Genomics evidence files in SAM format
      • New plug-in for gapped read mapping of e.g. cDNA to genomes
    • New plugin to detect Structural variation
      • Action to detect structural genomic variation from paired read information
      • Action to detect copy-number variation (CNV) from coverage information
    • New and more flexible data structures to store information about paired data
    • All history entries will from now on include the version number of the software
    • Previous limit at 2 billion for the maximum number of reads in one analysis has been removed.
    • Reporting of amino acid changes in SNP and DIP detection now follows recommended nomenclature more closely w.r.t. changes that affect start codons and changes that cause indels at the amino acid level.
    • Performance of Excel 2010 exporter improved in terms of speed and memory requirements
    • Export of trace data in scf format.


    QIAGEN CLC Genomics Server 3.1.1

    Release date: 2011-04-06

    RNA-Seq would crash when selecting prokaryote as organism type


    QIAGEN CLC Genomics Server 3.1

    Release date: 2011-04-05

    New and improved features

    • Support for PBS Pro in addition to Oracle Grid Engine. Read more.
    • Import of Ion Torrent data. A special importer has been made for Ion Torrent data in fastq or sff format. Read more.
    • Grid integration redesigned to be more stable and easier to deploy. Existing users of the grid integration please contact support@clcbio.com for upgrade instructions.
    • Import through Command Line Tools now works on grid set-ups. Read more.
    • Reporting merged SNPs is now optional. Read more.
    • SNP detection: When minimum paired coverage is set, reads from broken pairs will be completely ignored. Read more.
    • RNA-Seq: the transcript-level sample includes a column for the ratio of unique to total transcript reads. Note that this means that results generated with this version cannot be used in older versions. Read more.
    • Better support for color space SAM/BAM files.
    • Export in color space fastq format. When data is marked as color space, exporting in fastq format will produce a file with color encoding rather than bases.
    • Error reports from grid workers now include log files
    • Audit log files are archived to files every three months
    • Faster submission of bug report archives
    • List of grid presets in the Workbench dialog is now sorted, and the last selection of preset is preserved so that the first step can be skipped

    Bug fixes

    • Fixed: The Gridworker would run out of memory on computers with large amounts of memory
    • Fixed: Import of csfasta paired data crashed when one read had a dot in the beginning of the sequence.
    • Import of paired qseq files: the read pairs are now joined correctly when importing paired qseq files
    • Fixed: Import of GO annotation files did not work
    • When processing tagged paired data sets, the status of the resulting files were not marked as paired. This means that subsequent analyses did not make use of the paired information.
    • Various minor bug fixes
    Please note that you need to upgrade the Workbench plug-in in order to connect to the new server and you will also need to update the Command Line Tools client


    QIAGEN CLC Genomics Server 3.0.1

    Release date: 2011-02-18

    Bug fixes

    • CHiP-seq analysis adjusted for the use of gapped aligner – CHiP-seq analysis with previous version should be redone
    • Improved support for Mac OS X systems with japanese language


    QIAGEN CLC Genomics Server 3.0

    Release date: 2011-01-26

    New features

    • New way of running analyses on the server. Previously each analysis tool was duplicated in the Toolbox, but now the first step in the analysis wizard is about where the analysis should run.
    • Command Line Tools (will be available for beta test at selected customers medio January 2011)
      • A command line-based alternative to the Workbench as client
      • Enables using the server tools in a scripting environment
      • Note that this is not a stand-alone command line program – it is a client to the server
    • Oracle Grid Engine support (will be available for beta test at selected customers medio January 2011)
      • Jobs can be run on Oracle Grid Engine (formerly known as Sun Grid Engine)
      • Job status can be monitored from the Workbench
      • Seamless integration in the Workbench clients
    • External Applications re-design Read more
      • Sample scripts and configurations for Bowtie and Velvet integration available for download
      • New option to export and import external application configuration settings
      • New options for post-processing of analysis results see an example
      • New overview of parameter flows Read more
    • Check set-up tool for diagnostics of server setup Read more
    • Batching functionality of all high-throughput sequencing tools. It is now possible to start batch runs, e.g. running 12 samples through RNA-Seq Analysis in one go. Read more.
    • RNA-seq: transcript-level expression values and support for paired data
      • Included option to use paired information in RNA-seq. Read more.
      • Expression values can now be stratified into transcript level expression values, both for single and paired reads. Read more.
      • SOLiD data: new algorithm for mapping reads allows much higher fraction of reads to be mapped. Rather than a score limit, you now specify the stringency of the mapping using length and similarity fractions. Read more.
      • Similarity fraction for mapping of long reads is now available as a user-specified option (this was previously automatically set). Read more.
      • Simple reporting of putative gene fusions when using paired data. Read more.
      • Note about compatibility: Results from earlier versions should not be compared with results from this version.
    • SOLiD data: new algorithm for mapping reads allows much higher fraction of the reads to be mapped.
      • Rather than a score limit, you now specify the stringency of the mapping using length and similarity fractions. Read more..
      • Note about compatibility: Results from earlier versions should not be compared with results from this version.
    • Multiplexing: Process tagged sequencing data
      • De-multiplexing tool is now running on the server Read more
      • It is now possible to import and use a file with bar codes and sample names. This makes it easier to process data with a high number of multiplexed samples. Read more.
      • You can specify separate output folders for each sample, making it convenient to batch process the subsequent analyses.
    • High-throughput Sequencing Import includes an option to place data into sub-folders (useful for batching subsequent analyses)
    • SNP detection reports adjacent SNPs within the same codon as one SNP. Read more.
    • De novo assembly: post-processing options when mapping reads back to contig sequences have been expanded. It is now possible to preserve the original contig sequences from the assembler (they used to be replaced by the consensus sequence from the mapping). Read more.
    • Support for exporting tables as tab-delimited files.
    • Memory allocation: the default memory allocation for the Server changes from 75% to 50% of available physical memory with a maximum at 50 GB.
    • New way of getting a license based on Order ID and automatic download of a license file. This makes it much easier to set up the server.
    • New licensing model replacing the Small, Medium and Large business editions.

    Bug fixes

    • SNP detection bug with corrupt complementary CDS annotations.
    • SNP detection: color correction errors now count when filtering SNPs (this has become important with the new mapping algorithm for SOLiD data).
    • Time out in the communication between Workbench and Server is now recovered in most situations.
    • Various bug-fixes


    QIAGEN CLC Genomics Server 2.6

    Release date: 2010-10-28

    Improvements

    • Create detailed mapping report now available on server

    Bug fixes

    • SNP and DIP detection previously ignored overlapping pairs. Now they count (as one read) if the fulfill the quality criteria (SNP detection). In cases where the two parts of the pair disagree, the pair does not count. We recommend running all SNP and DIP detections based on overlapping pairs data sets again (this would be the case if the minimum distance when mapping the reads is lower than two times the read length). There is no need to re-run mappings – just the SNP/DIP detection.
    • ChIP-Seq: “nearest gene” reported not always right. This was the case for the last peak on each chromosome and also in cases where the order of the gene annotations in the reference file did not correspond to the order of the annotations on the actual sequence. We recommend running all ChIP-Seq Analyses again to get the correct reporting of nearest genes. There is no need to re-run the mappings.
    • Color space check box not checked per default when running color space data. We recommend checking the history of mappings based on color space data. If the history shows “Color space alignment = No”, you should re-run the mapping and consequent analyses.
    • Improved import of SAM/BAM files:
      • Better support for files from SOLiD Bioscope
      • Preliminary support for Complete Genomics files (The actual alignment is not represented completely – insertions that relates to a consensus sequence will be represented as unaligned ends in the imported mappings. This should be taken into account when looking for variations.)
    • Going from step 2 to 3 in SNP detection wizard took a long time when using data with many references/contigs
    • Various minor bug fixes


    QIAGEN CLC Genomics Server 2.5.3

    Release date: 2010-08-25

    Bug fixes

    • Fixed error when importing 454 SFF files
    • Fixed error when importing SOLiD data with quality scores when the reads had “.”
    • Fixed error mapping large data sets on Windows 64-bit systems
    • Genbank export of annotations on the negative strand were not in the right order
    • Fixed memory and performance issues related to import of many sequences, eg. from ACE files.
    • Fixed problem with SNP detection on large data sets suddenly running very slow.
    • Better support for html when exporting tables to Excel.
    • Various minor bug fixes
     


    QIAGEN CLC Genomics Server 2.5.2

    Release date: 2010-07-05

    Bug-fixes

    • Fixed a problem resulting in a “node communication error” when using built-in authentication and job nodes
    • Fixed a problem using initial bind credentials with LDAP authentication


    QIAGEN CLC Genomics Server 2.5.1

    Release date: 2010-06-30

    Bug-fixes

    • Resolves problem with SAM/BAM import
    • Resolves problem with import of tabular mapping files
    • Missing FastQ export included
    • Scalability improvements in mapping and de-novo assembly with drastic improvements in performance


    QIAGEN CLC Genomics Server 2.5

    Release date: 2010-06-15

    New features

    • New de novo assembly algorithm. Read more 
    • Small RNA Analysis 
      • Brand new tool for analyzing small RNA (including miRNA) data sets
      • Adapter trimming
      • Counting of tags
      • Annotation using miRBase and other resources
      • Visualization of miRNA variants
      • Expression analysis
    • Server-side import of High-throughput Sequencing Data. Read more
    • Trim sequences is now available on the server. Read more 
    • Renaming and redefining concepts
      • Reference assembly -> Read mapping. We adjust to the common term used today for aligning sequencing reads to a reference sequence.
      • Contig -> Read mapping. The result of read mapping was previously called a contig (i.e. the alignment of reads to a reference sequence). Now, the term “contig” is used exclusively for results from de novo assembly. The result of mapping reads is called a “read mapping”.
      • Paired-end -> Paired. We now distinguish during import between Paired-end and Mate pair data. Once imported, there is no difference, and they are both called “Paired”.
    • Improved SAM/BAM import :
      • BAM format now supported, both import and export
      • More robust implementation
      • Better performance
      • Preview panel making it easier to match reference and SAM/BAM file
      • Reference sequence name spaces automatically converted to underscores when comparing with SAM/BAM file
    • High-throughput Sequence Data Import
      • Gzip support
      • SOLiD fastq format supported (when downloading SOLiD data from Sequence Read Archive, SRA). Read more 
      • 454 paired data: Support for both FLX and Titanium linkers (also the possibility to add custom non-palindromic linkers). Read more 
      • Improved support for SOLiD paired-end data. Read more 
      • Support for data from Illumina Pipeline 1.5. Read more 
      • Import of tabular alignment files: it is now possible to specify a read name from the file to be imported with the read. Read more 
    • Better compression of reference sequences (lower memory footprint and disk space usage)
    • Performance improvement of read mapping algorithm
    • Improved memory management in general: lower memory footprint and shorter management overhead pauses.
    • Improved memory handling of large tabular data sets.
    • RNA-Seq:
      • Directional RNA-Seq. Read more 
      • Exon-intron reads are now counted under Total exon reads. When comparing new and old samples, please re-run the analysis on the old samples to ensure consistency. Read more .
    • SNP and DIP detection :
      • Dialog usability improved by adding an advanced panel for advanced users
      • Minimum counts have been made more clear by creating a Minimum and Sufficient count
    • Performance of ACE export improved, especially for long reference sequences or read mapping tables.
    • It is now possible to pause and restart processes involving read mapping and de novo assembly (except the accelerated mapping part of the analyses). Read more 
    • When searching data from the Workbench, the results did not list the custom attributes of the data. Read more .
    • Copy operations on server locations are now performed completely on the server side, eliminating client processing and network traffic
    • A number of import and export formats have been included on the server, including csv, ace and excel.
    • Progress when downloading files from the server using the web interface is shown in browser
    • External applications:
      • Added option to allow external application processes to run as master processes (no blocking of the queue). Read more
      • Command line call is now part of error message when an external application fails. Read more
    • Performance of export of data via the Workbench from a server location has been improved
    • Index server status added under User Statistics in the Admin tab of the web interface.
    • Possibility to report server-side bugs from both web interface and Workbench, including log and configuration files. Read more
    • Improved usability of user interface for adding locations in the web interface. Read more
    • Server home path has been removed from configuration panel in the web interface (it now resides in a properties file in the settings directory). This makes it easier to deploy a job node installation in a mixed environment.

    Bug-fixes

    • Added support for viewing data attributes in web browser for enzyme lists.
    • Job nodes failed to start when master server was not already running.
    • Display of folder structure was not right in special cases involving differentiated permission on folders
    • Changed order of custom attributes was not reflected in search drop-down menu
    • Searching for data entered as custom attributes required specification of which attribute to search in
    • Read mapping: fixed windows errors on large data sets, fixed color space errors
    • RNA-Seq: max number of mismatches when running color space data could be set to three in the dialog but did not take effect. Now the limit at 2 is enforced in the dialog.
    • Genbank import: sequence name (LOCUS) was truncated to 18 characters


    QIAGEN CLC Genomics Server 2.0.1

    Release date: 2010-02-04

    Bug fixes

    • A few import formats was missing on the server (when importing using the API and the web interface)
    • RNA-seq: reads that extend over more than two exons are now shown correctly
    • Names of results from reference assemblies are now named according to the input data
    • Various bug fixes


    QIAGEN CLC Genomics Server 2.0

    Release date: 2009-12-15

    New features

    • Support for Job Nodes. Parallelized Job Execution (on Command level) with flexible/scalable multi job node setup. Advanced configuration of job nodes on command level.
    • 3 tier data communication. Data communication/management is now based on communication through the Server middleware.
    • Option for File locations on server.
    • Index Server for stability/scalability.
    • Command Line Integration tool on server side for invocation through user friendly UI on Workbench. Includes example (ClustalW)
    • All High throughput sequencing data importers are now on the Server. That is “Roche 454″, “Illumina”, “SOLiD”, “Fasta/Helicos”, “Sanger”, “SAM Assembly Files”, “Tabular Assembly Files (ELAND format)”
    • RNA-Sequencing can now be run on the Server. Read more…
      • The analysis including mapping of reads, distributing non-specific matches and calculating expression values are done on the server
      • Visualization is done in the Workbench
      • Statistical analysis of the results are done in the Workbench (these are not heavy calculations)
    • Administrators can close user sessions. Read more…
    • Option to automatically log in to the server when the Workbench starts Read more…
    • The order of attributes can now be changed. Read more…
    • Finished server processes are removed when closing down the Workbench. Running processes will be shown next time the Workbench connects to the server.
    • Global alignment for long reads when running reference assembly algorithm
    • Gapped color-space alignment when running reference assembly
    • Significantly improved speed of all operations with large data sets
    • The unassembled reads from an assembly now preserves their paired-end status (this also means that you can get two lists – one with pairs and one with the remainder of the broken pairs
    • SNP detection output table now reports if multiple non-synonymous SNPs exist in same codon
    • SNP detection dialog: Quality filtering is no longer disabled when quality scores are missing. Due to performance issues it is not possible to check if quality scores are present. The SNP detection will just omit the quality score filtering if quality scores are not present.
    • SNP detection: possible to detect variants with frequency less than 1 percent.
    • General import and export
      • Export tables and reports in Excel format.
      • Import section of user manual re-structured to provide better overview Read more…. Expression data importers are now described in technical details in a separate section Read more….
      • You can now export multiple sequence lists in fasta format
      • Forced import of zip files is now supported (it will force import the contents of the zip file)
      • The standard import now accepts gzip and tar files as well as zip
      • Genbank importer now makes several attempts at naming genes that do not have a gene name. It will iteratively try the following qualifiers: “product”, “locus_tag”, “protein_id” and “transcript_id”
      • When importing genbank files where the length stated does not match the actual sequence, a warning is shown but the sequence is accepted.

    Bug-fixes:

    • Fixed an error opening external files from a server location


    QIAGEN CLC Genomics Server 1.6.1

    Release date: 2009-08-21

    New features

    • Export of annotations in GFF format (joined regions not supported)
    • Export of sequence data in fastq format

    Bug-fixes:

    • Fixed problems importing expression annotation files
    • Various bug-fixes
    This update is recommended for all users.